ongoing

docs/use.rst

@@ -11,10 +11,10 @@ cancel the execution of the workflow.
 Submitting workflow
 -------------------
 
-*Decimate* **dbatch** command accepts the same `options`_ as the SLURM
+*Decimate* **dbatch** command accepts the same options_ as the SLURM
 **sbatch** command and extends it in two ways:
 
-.. _options: https://slurm.schedmd.com/sbatch.html
+.. _options: 
 
  - it transparently submits the user job within a fauit-tolerant framework
  - it adds new options to manage the workflow execution if a problem occurs
@@ -31,5 +31,64 @@ Submitting workflow
 How to submit
 -------------
 
->>> print "This is a doctest block." 
-This is a doctest block.
+Let *my_job.sh* be the following example job:
+
+::
+
+  #!/bin/bash
+  #SBATCH -n 1
+  #SBATCH -t 0:05:00
+   
+
+  echo job running on...
+  hostname
+  sleep 10
+
+  echo job DONE
+
+If not done yet, we first load the *Decimate* module:  
+
+::
+
+   module load decimate
+
+Then submission of jobs follows the same syntax than with the **sbatch** command:   
+
+::
+    
+   dbatch --job-name=job_1 my_job.sh
+
+::
+
+   [MSG  ] submitting job job_1 (for 1) --> Job # job_1-0-1 <-depends-on None 
+   [INFO ] launch-0!0:submitting job job_1 [1] --> Job # job_1-0-1 <-depends-on None
+   Submitted batch job job_1-0-1
+   [1] --> Job # job_1-0-1 <-depends-on None
+
+::
+   
+   dbatch --dependency=job_1  --job-name=job_2 my_job.sh
+   [INFO ] launch-0!0:Workflow has already run in this directory, trying to continue it
+   [MSG  ] submitting job job_2 (for 1) --> Job # job_2-0-1 <-depends-on 218459 
+   [INFO ] launch-0!0:submitting job job_2 [1] --> Job # job_2-0-1 <-depends-on 218459
+   Submitted batch job job_2-0-1
+   [1] --> Job # job_2-0-1 <-depends-on 218459
+
+::
+   
+   dstat
+
+::
+   
+   [MSG  ] step job_1-0:1-1                  SUCCESS   SUCCESS:  100% 	FAILURE:   0% -> [] 
+   [MSG  ] step job_2-0:1-1                  RUNNING   SUCCESS:    0% 	FAILURE:   0% -> [] 
+
+::
+
+   dstat
+   [MSG  ] CHECKING step : job_2-0 task 1  
+   [INFO ] launch-0!0:no active job in the queue, changing all WAITING in ABORTED???
+   [MSG  ] step job_1-0:1-1                  SUCCESS   SUCCESS:  100% 	FAILURE:   0% -> [] 
+   [MSG  ] step job_2-0:1-1                  SUCCESS   SUCCESS:  100% 	FAILURE:   0% -> [] 
+
+

module/decimate.template

@@ -25,14 +25,15 @@ set-alias dsa "decimate  -sl"
 set-alias de  "decimate --explore "
 
 
-set-alias se        "dbatch --decimate --explore "
-set-alias sb        "dbatch"
-set-alias sl        "dbatch --decimate -l"
-set-alias slog      "dbatch --decimate -l"
-set-alias ss        "dbatch --decimate -s"
-set-alias sstatus   "dbatch --decimate -s"
-set-alias ssa       "dbatch --decimate -sa"
-set-alias ssl       "dbatch --decimate -sl"
+set-alias de        "dbatch --decimate --explore "
+set-alias db        "dbatch"
+set-alias dl        "dbatch --decimate -l"
+set-alias dlog      "dbatch --decimate -l"
+set-alias ds        "dbatch --decimate -s"
+set-alias dstat     "dbatch --decimate -s"
+set-alias dkill     "dbatch --decimate --kill"
+set-alias dsa       "dbatch --decimate -sa"
+set-alias dsl       "dbatch --decimate -sl"
 
 prepend-path PYTHONPATH $DECIMATE_PATH
 prepend-path PATH $prefix/bin

tests/my_job.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+#SBATCH -J yyy123
+#SBATCH -p debug
+#SBATCH -n 1
+#SBATCH -t 0:01:00
+
+
+echo job running on...
+hostname
+sleep 10
+
+echo job DONE